[R-sig-ME] glmer syntax for model with "common" random effects
martin.stjernman at biol.lu.se
Fri May 16 11:22:46 CEST 2014
Am I completely off track claiming that (Norm_Combined|Pat_ID/Proc_ID) is equivalent to (Norm_XY :Norm_21|Pat_ID/Proc_ID) rather than to (Norm_XY * Norm_21|Pat_ID/Proc_ID) in the post by Thierry?
Norm_XY*Norm_21 would expand to Norm_XY + Norm_21 + Norm_XY:Norm_21 wouldn't it?
(Just to understand the formula specifications in R)
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From: r-sig-mixed-models-bounces at r-project.org [mailto:r-sig-mixed-models-bounces at r-project.org] On Behalf Of ONKELINX, Thierry
Sent: den 16 maj 2014 10:24
Cc: r-sig-mixed-models at r-project.org
Subject: Re: [R-sig-ME] glmer syntax for model with "common" random effects
Please keep the mailing list in cc. Others might chime in and you might get a faster reply.
You need to create a variable the combines both norms. That is what Norm_Combined <- interaction(Norm_XY, Norm_21) does. Then you could do glmer(Sex ~ 1 + Norm_XY + Norm_21 + (Norm_Combined|Pat_ID/Proc_ID), data = PGD_21.df,family = binomial). Note that this would be equivalent to glmer(Sex ~ 1 + Norm_XY + Norm_21 + (Norm_XY * Norm_21|Pat_ID/Proc_ID), data = PGD_21.df,family = binomial). So even more complex than your original model.
Note that (1|A/B) is equivalent to (1|A + 1|A:B) Therefor my suggestion to use (1|Pat_ID) + (1|PatID:Proc_ID) + (1|Pat_ID:Norm_Combined) + (1|PatID: Proc_ID:Norm_Combined) which is the verbatim of (1|PatID/Proc_ID/Norm_Combined) + (1|PatID/ /Norm_Combined). This model allows the same fit as (Norm_Combined|Pat_ID/Proc_ID) but assumes that all levels of Norm_Combined come from a univariate iid normal distribution (same variance and uncorrelated). (Norm_Combined|Pat_ID/Proc_ID) assumes that the levels of Norm_Combined come from a multivariate normal distribution. And hence requires a lot more parameters.
If this is not what you want, then give us the mathematical equation of the model that you need.
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance Kliniekstraat 25
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Thierry.Onkelinx at inbo.be
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Van: orzack [mailto:orzack at freshpond.org]
Verzonden: woensdag 14 mei 2014 15:20
Aan: ONKELINX, Thierry
Onderwerp: RE: [R-sig-ME] glmer syntax for model with "common" random effects
many thanks for your suggestion. I think we are talking past each other, which is likely mostly due to my not being clear and/or my not understanding your suggestion. Perhaps this would help clarify:
in my first email, I presented this model
>model <- glmer(Sex ~ 1 + Norm_XY + Norm_21 + ((Norm_XY +
>Norm_21)|Pat_ID/Proc_ID), data = PGD_21.df,family = binomial))
this generates a "common" or "overall" estimate of the intercept, i.e., one that estimates the random effects for both predictors combined. What I would like is a model that provides a similar "combined" estimate for the slope. it would be something like
>model <- glmer(Sex ~ 1 + Norm_XY + Norm_21 +
>((COMBINEDNORM)|Pat_ID/Proc_ID), data = PGD_21.df,family =
so that the fixed effects are calculated separately but norm-specific estimates of the random effects for the slope were not provided.
When I use the interaction approach you mention, glmer returns estimates for each combination of the levels
>I think you want something like this (if I understand you question correctly).
>PGD_21.df$Norm_Inter <- interaction(PGD_21.df$NormXY,
>PGD_21.df$Norm_21) model <- glmer(Sex ~ 1 + Norm_XY + Norm_21 + (1|Pat_ID) + (1|PatID:
>Proc_ID) + (1|Pat_ID:Norm_Inter) + (1|PatID: Proc_ID:Norm_Inter), data
>= PGD_21.df,family = binomial)
I want to reduce the AIC penalty. This increases it unless I misunderstand your syntax. Speaking of which, what does this syntax mean
In my problem, only PatID and Proc_ID provide estimates of random effects.
I look forward to hearing from you.
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